added groups option to read.otu, added qtrim option to trim.seqs, fixed bug in get...

[mothur.git] / getlinecommand.cpp

diff --git a/getlinecommand.cpp b/getlinecommand.cpp
index a7ca17fc34297c58869f0d578f52ec70e1fc3367..f1ec55cab12261a5b91f425553bf34bc71393727 100644 (file)
--- a/getlinecommand.cpp
+++ b/getlinecommand.cpp
@@ -3,26 +3,47 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 1/30/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "getlinecommand.h"
 
-
-GetlineCommand::GetlineCommand(){
+//**********************************************************************************************************************
+GetlineCommand::GetlineCommand(string option){
        try {
                globaldata = GlobalData::getInstance();
+               abort = false;
+               
+               //allow user to run help
+               if(option == "help") { help(); abort = true; }
+               
+               else {
+                       if (option != "") { mothurOut("There are no valid parameters for the get.line command."); mothurOutEndLine(); abort = true; }
+                       
+                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the get.line command."); mothurOutEndLine(); abort = true; }                                
+               }
+
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GetlineCommand class Function GetlineCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "GetlineCommand", "GetlineCommand");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the GetlineCommand class function GetlineCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void GetlineCommand::help(){
+       try {
+               mothurOut("The get.line command can only be executed after a successful read.otu command.\n");
+               mothurOut("You may not use any parameters with the get.line command.\n");
+               mothurOut("The get.line command should be in the following format: \n");
+               mothurOut("get.line()\n");
+               mothurOut("Example get.line().\n");
+       }
+       catch(exception& e) {
+               errorOut(e, "GetlineCommand", "help");
                exit(1);
-       }       
-                       
+       }
 }
 
 //**********************************************************************************************************************
@@ -34,37 +55,35 @@ GetlineCommand::~GetlineCommand(){
 
 int GetlineCommand::execute(){
        try {
-               filename = globaldata->inputFileName;
+       
+               if (abort == true) { return 0; }
+       
                ifstream in;
-               openInputFile(filename, in);
+               openInputFile(globaldata->inputFileName, in);
                string label;
                int numBins = 0;
                int count = -1;
                int line = 1;
-               while(in.good())
-               {
+               while(in.good()) {
                        if(count > numBins)
                                count = 0;
-                       if(count == 0)
-                       {
-                               cout << line << "\n";
+                       if(count == 0) {
+                               mothurOut(toString(line)); mothurOutEndLine();
                                in >> numBins;
                                line++;
                        }
                        in >> label;
                        count++;
                }
+               
+               in.close();
                return 0;               
        }
 
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GetlineCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "GetlineCommand", "execute");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the GetlineCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }